Package: metagenomeFeatures

Version: 1.10.0

Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings metagenomeFeatures_1.10.0.tar.gz

StartedAt: 2018-04-12 00:54:53 -0400 (Thu, 12 Apr 2018)

EndedAt: 2018-04-12 00:58:09 -0400 (Thu, 12 Apr 2018)

EllapsedTime: 195.8 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: metagenomeFeatures.Rcheck

Warnings: 1

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### Running command:
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###   /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings metagenomeFeatures_1.10.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/metagenomeFeatures.Rcheck’
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘metagenomeFeatures/DESCRIPTION’ ... OK
* this is package ‘metagenomeFeatures’ version ‘1.10.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘metagenomeFeatures’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  9.8Mb
  sub-directories of 1Mb or more:
    data      2.1Mb
    extdata   6.7Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.mgDb_annotateFeatures: no visible binding for global variable
  ‘db_keys’
.select.taxa: no visible binding for global variable ‘Keys’
.select.taxa: no visible binding for global variable ‘.’
aggregate_taxa: no visible binding for global variable ‘.’
aggregate_taxa: no visible binding for global variable ‘index’
vignette_pheno_data: no visible global function definition for
  ‘read.csv’
Undefined global functions or variables:
  . Keys db_keys index read.csv
Consider adding
  importFrom("utils", "read.csv")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
  ‘msd16s_metagenomeAnnotation’ ‘msd16s_query_df’
Undocumented data sets:
  ‘msd16s_metagenomeAnnotation’ ‘msd16s_query_df’
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.6-bioc/meat/metagenomeFeatures.Rcheck/00check.log’
for details.

* installing *source* package ‘metagenomeFeatures’ ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (metagenomeFeatures)

R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> 
> test_check("metagenomeFeatures")
Loading required package: metagenomeFeatures
Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colMeans, colSums, colnames, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
    pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
    setdiff, sort, table, tapply, union, unique, unsplit, which,
    which.max, which.min

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: limma

Attaching package: 'limma'

The following object is masked from 'package:BiocGenerics':

    plotMA

Loading required package: glmnet
Loading required package: Matrix
Loading required package: foreach
Loaded glmnet 2.0-16

Loading required package: RColorBrewer

Attaching package: 'dplyr'

The following object is masked from 'package:Biobase':

    combine

The following objects are masked from 'package:BiocGenerics':

    combine, intersect, setdiff, union

The following object is masked from 'package:testthat':

    matches

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

══ testthat results  ═══════════════════════════════════════════════════════════
OK: 90 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
 10.264   0.160  10.452 

name	user	system	elapsed
MgDb-class	0.2	0.0	0.2
aggregate_taxa	1.876	0.020	1.910
annotateFeatures-MgDb-method	0.392	0.028	0.419
annotateMRexp_fData-MgDb-method	0	0	0
get_demoMgDb	0.080	0.004	0.084
get_mockMgDb	0.084	0.000	0.086
mgF_meta	0.028	0.000	0.028
mgF_seq	0.092	0.004	0.096
mgF_taxa	0.028	0.000	0.028
mgF_tree	0.032	0.000	0.033
mgFeatures-class	0.000	0.000	0.001
mgQuery	0.000	0.004	0.001
mgdb_meta	0.084	0.004	0.088
mgdb_seq	0.124	0.000	0.126
mgdb_taxa	0.352	0.000	0.371
mgdb_tree	0.100	0.000	0.101
mock_mgF	0.000	0.000	0.001
mock_query_df	0.000	0.000	0.001
select-MgDb-method	0.608	0.004	0.613
taxa_columns	0.084	0.000	0.085
taxa_keys	0.104	0.012	0.119
taxa_keytypes	0.092	0.000	0.092
taxa_levels	0.108	0.008	0.118